the structure and design of DNA matches up nicely with the design patterns used by software engineers (like WK!)

There are some very good tips in this lecture so that you will be able to explain intelligent design to others in simple ways, using everyday household items and children’s toys to symbolize the amino acids, proteins, sugar phosphate backbones, etc.

Proteins are constructed from a sequence of amino acids:

A sequence of amino acids forming a protein

Proteins sticking onto the double helix structure of DNA:

Some proteins sticking onto the sugar phosphate backbone

I highly, highly recommend this lecture. You will be delighted and you will learn something.

Here is an article that gives a general overview of how intelligent design challenges. If you want to read something more detailed about the material that he is covering in the lecture above related to the origin of life, there is a pretty good article here.

UPDATE: There is a good breakdown of some of the slides with helpful flow charts here on Uncommon Descent.

Stephen Meyer is a leading proponent of Intelligent Design who directs the Centre for Science and Culture at the Discovery Institute in Seattle. His [first] book “Signature in the Cell” claims to show that the DNA code is the product of intelligent mind, not naturalistic processes. Keith Fox is Professor of Biochemistry at Southampton University. He chairs the UK Christians in Science network but disagrees strongly with ID. They debate how life could have originated and whether design is allowed as an explanation in science.

Summary: (stuff in italics is my snarky paraphrase)

Meyer:

background and how he got interested in intelligent design

his research focus is on the origin of life – the first replicator

summarizes the history of origin of life studies

authored the book “Signature in the Cell”

the DNA enigma: where did the information in DNA come from?

naturalistic explanations of the DNA information have failed

but intelligent agents are known to be able to produce information

the best explanation of the information in DNA is that an intelligent agent authored it

Meyer’s book was named by atheist philosopher of science Thomas Nagel as a Times Literary Supplement Book of the Year in 2010

why is design so controversial? Many people think that Darwin explained why nature appears design

the Darwinian view is that nature can create the appearance of design using mutation and selection

however, Darwinian mechanisms cannot explain the origin of the first living cell, it assumes replication, and the origin of life is about where the first replicator comes from

Fox:

Meyer’s argument is not about the evolution of life after the first cell

Meyer’s case for design is about the origin of life

naturalists do not know a naturalistic explanation for the origin of life

there are a number of naturalistic hypotheses for the origin of life, like the RNA-first hypothesis

maybe in a few years one of them will turn out to be correct

what intelligent design is arguing from a gap in our current naturalistic knowledge to infer that God intervened in nature

Meyer:

that’s not what intelligent design is at all

the approach ID theorists use is the inference to best explanation

you evaluate all explanations, non-intelligent causes and intelligent causes

you prefer the best possible explanation

we know that minds are capable of producing information just like the information we find in DNA

Fox:

living cells replicate, so they have the ability to introduce mutations as they replicate and then some of those mutations can be selected

so maybe the process of replicating that living cells do created the first living cell

maybe the first living cell created itself, X brought X into being, self-creation, what’s irrational about that?

Meyer:

the issue is the origin of life – where did the first living cell come from?

you cannot appeal to the operations that a living cell can perform to explain the origin of the first living cell

there was no first living cell operating before the first living cell

there was no replication, mutation or selection before the first living cell

in fact, in my book I show that there is no known naturalistic mechanism that is able to produce the information needed for the first living cell

nothing can create itself, that is self-contradictory

Fox:

Well, you are just saying that because something is complex that God did it

Meyer:

Sadly, no. What I actually said needed to be explained was the information, not complexity

And we know from software engineering that the process of adding information to code is performed by programmers

in the absence of any adequate naturalistic explanation for information, we are justified in taking the explanation that we are familiar with – namely, intelligent agency – based on our uniform, universal experience of what causes information

Fox:

well, maybe we can appeal to the mutation and selection in existing living cells to explain the origin of the first living cell

maybe there were living cells before the first living cell, and then these other living cells created the first living cell

Meyer:

we can’t keep invoking mutation and selection when those processes are not operating prior to the origin of the first living cell

Fox:

well maybe some bare-bones self-replication molecule was a precursor to the first living cell

Meyer:

even to generate very limited replicator would require a large amount of information

the argument I am making is – where does the evolution come from?

Fox:

well, maybe we will think of an explanation for information that is naturalistic in 20 years

we’ve thought of explanations to things that were NOT information before

so maybe we will be able to think of something to explain information based on our ability to explain NOT information before

Moderator: Change topics: the Dover decision

Meyer:

the Discovery Institute opposed the policy that causes the trial

the wording of the statute was poor

the judge was completely wrong in his decision

young earth creationists used the phrase “intelligent design” to cover their agenda

intelligent design is an inference using the normal methods of science

Fox:

intelligent design is a science stopper because it stops looking for a naturalistic explanation

everything in nature must have a naturalistic explanation

everything has to be explained using matter and time and chance

it just has to be that way!!!!

Meyer:

well, what luck would you have explaining an effect like Mt. Rushmore?

can you explain that using matter,time and chance?

Mt. Rushmore was the product of intelligence, not wind and erosion

similarly, there is information in the cell, and we know that intelligence causes information

Fox:

So you are saying that we don’t understand and therefore an intelligence is necessary?

Meyer:

no I am saying we DO understand and we are making an inference based on that understanding

you are the one who is insisting on a material explanation because you pre-suppose materialism

we know that minds have causal powers, and we can infer mind as an explanation from information

Fox:

well nature is a seamless chain of material causes and effects

Meyer:

agents can act without violating the laws of nature

even humans can act as intelligent agents to create information in books, and they don’t violate the laws of nature

intelligent causes are real, and they explain effects in nature

Fox:

you’re trying to impose on science something to do with meaning and purpose

Meyer:

no that’s not what we’re doing, we’re inferring from from the fact that we ourselves are known causes of information to the fact that an intelligence cause is the best explanation for information in the cell

Fox:

but I am a materialist, I need a materialist explanation

Meyer:

mind IS an answer to the how question

we infer to mind in many other scientific disciplines, like cryptography, archaeology, etc.

a materialist might accuse an archaeologist of engaging in a “scribe-of-the-gaps” argument, but the best explanation of an artifact with information is a scribe

we are inferring that mind is the cause from the nature of the effect: information

Moderator: is it appropriate to call DNA “information”

Fox:

well DNA is just a molecular polymer, any reference to information is just by analogy

Meyer:

DNA is a molecular polymer, but it also exhibits the property of specified complexity

the arrangement of bases, which function as machine instructions in a software program, for performings task in the cell

we have observed that the property of specified complexity always comes from an intelligence

Fox:

well, maybe there are other sequences that would work, so maybe it’s really not uncommon to develop functioning sequences by chance alone, without an intelligence

Meyer:

you can measure how precise the functional specificity is in DNA and proteins

Moderator: is Shannon information the same as functional information

Meyer:

Shannon information refers to the sequences of digits or symbols that do not necessarily have any function, i.e. – a four character string QSZX has as much Shannon information as WORD. However, only the latter is functional against the pattern of the English language. There are arrangements of DNA bases and amino acids that have the same number of symbols/characters as a functional sequence would have, but they have no biological function – they do not exhibit specified complexity

Fox:

Well, maybe there are lots and lots of sequences of DNA and proteins so that it is fairly easy to get a functional one by chance

Meyer:

DNA sequences that are functional are extremely rare, protein sequences are even more rare

this is not my opinion, this is what the research shows – functional protein sequences are rare

Fox:

well maybe there are other functional sequences that are occur before the first functional sequence that are precursors to the first functional sequence

maybe there are billions of years of replication, mutation and selection before the first replication, mutation and selection

Meyer:

you can’t get to the first selectable functional sequence by appealing to precursor selectable functional sequences – there are no selectable functional sequences before the FIRST one

you have to get the first selectable functional sequence by chance alone, because there is nothing to mutate or select before the first replicator

the chance hypothesis has been rejected because the minimal amount of information for the simplest replicator is too high to get by chance alone, given the resources, including time, that are available

Moderator: Keith are you confident that naturalism will be able to substantiate these naturalism-of-the-gap speculations that you offer in response to Meyer’s actual science that we have today?

Fox:

well, it is hard to know for sure because it was just a fluke event

but there’s nothing irrational or unscientific or miraculous about it – the fluke would have a material explanation

there is nothing that we can detect that would implicate God, my speculations about a fluke which I cannot observe or measure or test would all be compatible with an atheistic worldview that omits God as a causal entity

Meyer:

where are those material processes that could account for this fluke then?

the whole point of this argument is that the information in DNA transcends the material components in the sequence

it’s the arrangement of the material parts/letters/characters/symbols/instructions that needs to be explained

Fox:

Well, I just have a different philosophy of science that rules out intelligent causation a priori

Meyer:

Yes, that’s the difference between us – you pre-suppose that all explanations of natural phenomena must exclude intelligent causes

There is a bit more where Meyer talks about how parts of the cell are implementations of various design patterns (Gang of Four design patterns) that are used by software architects who design software.

the structure and design of DNA matches up nicely with the design patterns used by software engineers (like WK!)

There are some very good tips in this lecture so that you will be able to explain intelligent design to others in simple ways, using everyday household items and children’s toys to symbolize the amino acids, proteins, sugar phosphate backbones, etc.

Proteins are constructed from a sequence of amino acids:

A sequence of amino acids forming a protein

Proteins sticking onto the double helix structure of DNA:

Some proteins sticking onto the sugar phosphate backbone

I highly, highly recommend this lecture. You will be delighted and you will learn something.

Here is an article that gives a general overview of how intelligent design challenges. If you want to read something more detailed about the material that he is covering in the lecture above related to the origin of life, there is a pretty good article here.

UPDATE: There is a good breakdown of some of the slides with helpful flow charts here on Uncommon Descent.

How likely is it that you could swish together amino acids randomly and come up with a sequence that would fold up into a functional protein?

Evolution News reports on research performed by Doug Axe at Cambridge University, and published in the peer-reviewed Journal of Molecular Biology.

Excerpt:

Doug Axe’s research likewise studies genes that it turns out show great evidence of design. Axe studied the sensitivities of protein function to mutations. In these “mutational sensitivity” tests, Dr. Axe mutated certain amino acids in various proteins, or studied the differences between similar proteins, to see how mutations or changes affected their ability to function properly.10 He found that protein function was highly sensitive to mutation, and that proteins are not very tolerant to changes in their amino acid sequences. In other words, when you mutate, tweak, or change these proteins slightly, they stopped working. In one of his papers, he thus concludes that “functional folds require highly extraordinary sequences,” and that functional protein folds “may be as low as 1 in 10^77.”11 The extreme unlikelihood of finding functional proteins has important implications for intelligent design.

And remember, you need a lot more than just 1 protein in order to create even the simplest living system. Can you generate that many proteins in the short time between when the Earth cools and the first living cells appear? Even if we spot the naturalist a prebiotic soup as big as the universe, and try to make sequences as fast as possible, it’s unlikely to generate even one protein in the time before first life appears.

Here’s Doug Axe to explain his research:

If you are building a protein for the FIRST TIME, you have to get it right all at once – not by building up to it gradually using supposed Darwinian mechanisms. That’s because there is no replication before you have the first replicator. The first replicator cannot rely on explanations that require replication to already be in place.

Here’s a paper published in the prestigious peer-reviewed science journal Nature, entitled “The oxidation state of Hadean magmas and implications for early Earth’s atmosphere”. This paper is significant because it undermines naturalistic scenarios for the origin of life.

A recent Nature publication reports a new technique for measuring the oxygen levels in Earth’s atmosphere some 4.4 billion years ago. The authors found that by studying cerium oxidation states in zircon, a compound formed from volcanic magma, they could ascertain the oxidation levels in the early earth. Their findings suggest that the early Earth’s oxygen levels were very close to current levels.

[…]Miller and Urey conducted experiments to show that under certain atmospheric conditions and with the right kind of electrical charge, several amino acids could form from inorganic compounds such as methane, ammonia, and water. Several experiments have been done using various inorganic starting materials, all yielding a few amino acids; however, one key aspect of all of these experiments was the lack of oxygen.

If the atmosphere has oxygen (or other oxidants) in it, then it is an oxidizing atmosphere. If the atmosphere lacks oxygen, then it is either inert or a reducing atmosphere. Think of a metal that has been left outside, maybe a piece of iron. That metal will eventually rust. Rusting is the result of the metal being oxidized. With organic reactions, such as the ones that produce amino acids, it is very important that no oxygen be present, or it will quench the reaction. Scientists, therefore, concluded that the early Earth must have been a reducing environment when life first formed (or the building blocks of life first formed) because that was the best environment for producing amino acids. The atmosphere eventually accumulated oxygen, but life did not form in an oxidative environment.

The problem with this hypothesis is that it is based on the assumption that organic life must have formed from inorganic materials. That is why the early Earth must have been a reducing atmosphere. Research has been accumulating for more than thirty years, however, suggesting that the early Earth likely did have oxygen present.

[…]Their findings not only showed that oxygen was present in the early Earth atmosphere, something that has been shown in other studies, but that oxygen was present as early as 4.4 billion years ago. This takes the window of time available for life to have begun, by an origin-of-life scenario like the RNA-first world, and reduces it to an incredibly short amount of time. Several factors need to coincide in order for nucleotides or amino acids to form from purely naturalistic circumstances (chance and chemistry). The specific conditions required already made purely naturalist origin-of-life scenarios highly unlikely. Drastically reducing the amount of time available, adding that to the other conditions needing to be fulfilled, makes the RNA world hypothesis or a Miller-Urey-like synthesis of amino acids simply impossible.

So here’s where we stand. If you are a materialist, then you need a reducing environment on the early Earth in order to get organic building blocks (amino acids) from inorganic materials. However, the production of these organic building blocks (amino acids) requires that the early Earth atmosphere be oxygen-free. And the problem with this new research, which confirms previous research, is that the early Earth contained huge amounts of oxygen – the same amount of oxygen as we have today. This is lethal to naturalistic scenarios for creating the building blocks of life on the Earth’s surface.

The “origin of life” (OOL) is best described as the chemical and physical processes that brought into existence the first self-replicating molecule. It differs from the “evolution of life” because Darwinian evolution employs mutation and natural selection to change organisms, which requires reproduction. Since there was no reproduction before the first life, no “mutation – selection” mechanism was operating to build complexity. Hence, OOL theories cannot rely upon natural selection to increase complexity and must create the first life using only the laws of chemistry and physics.

There are so many problems with purely natural explanations for the chemical origin of life on earth that many scientists have already abandoned all hopes that life had a natural origin on earth. Skeptical scientists include Francis Crick (solved the 3-dimensional structure of DNA) and Fred Hoyle (famous British cosmologist and mathematician), who, in an attempt to retain their atheistic worldviews, then propose outrageously untestable cosmological models or easily falsifiable extra-terrestrial-origin-of-life / panspermia scenarios which still do not account for the natural origin of life. So drastic is the evidence that Scientific American editor John Horgan wrote, “[i]f I were a creationist, I would cease attacking the theory of evolution … and focus instead on the origin of life. This is by far the weakest strut of the chassis of modern biology.”3

Most people who are talking about intelligent design at the origin of life talk about the information problem – how do you get the amino acids to form proteins and how do you get nucleotide bases to code for amino acids? But the starting point for solving the sequencing problem is the construction of the amino acids – there has to be a plausible naturalistic scenario to form them.